From kristofferm at drcmr.dk  Fri Apr  1 11:17:05 2022
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Fri, 1 Apr 2022 11:17:05 +0200
Subject: [Simnibs-discuss] designing tms coil
In-Reply-To: <CALXmJyHKaMWjNBExA3Gsdc4kNg2K428SGty-vUts=SOK4JS8mA@mail.gmail.com>
References: <CALXmJyHKaMWjNBExA3Gsdc4kNg2K428SGty-vUts=SOK4JS8mA@mail.gmail.com>
Message-ID: <CA+zwqSoiqmX9uRsyC2ydJD2HpgBK52tYFfdPAWnioE_VX35rcA@mail.gmail.com>

Well, that depends on how you want to approach this - what information do
you have available? What was typically done for coils previously was to
construct a dipole approximation using knowledge of the winding geometry.
This is what you find in the ccd files, the 3 first columns indicate the
dipole position in meters (in the coil coordinate system - coil center at
0,0,0 and z towards the head) and the last 3 columns indicate the dipole
moments in x,y and z directions respectively (for a flat coil this would
typically imply that only the third is different from zero).
If you have detailed and somewhat dense measurements of the magnetic field
you can look into:
https://pubmed.ncbi.nlm.nih.gov/26297386/
and the later dipole based approach:
https://arxiv.org/ftp/arxiv/papers/2112/2112.14548.pdf
Best,
Kristoffer

On Fri, 25 Mar 2022 at 20:29, mostafa abd elsamea <autofixegypt at gmail.com>
wrote:

> hello ,
> im trying to design a tms not in simnibs library,
> what is the tool should i use
> the second question is what is column name in the tms ccd file comes with
> simnibs
> thanks alot have a good day
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From kristofferm at drcmr.dk  Fri Apr  1 13:11:24 2022
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Fri, 1 Apr 2022 13:11:24 +0200
Subject: [Simnibs-discuss] Define coil orientation in Localite
Message-ID: <CA+zwqSqwxe5Nt3hCaptu=kTeappAOg4Kwmyb6-BxVZY7WSr5vA@mail.gmail.com>

The affine matrix indicates the transformation done to the coil coordinate
system in order to place it in the right position, hence the first 3
elements of the last column indicates the coil center position (typically
the location of the coil surface with highest A field) in the coordinate
system of the head model - so as you say.
The rotation is then given by the initial three elements of each of the
first three columns being unit vectors indicating x, y and z directions of
the coil in subject space.
If you want to express that in terms of angles you will have to decompose
into these - see for example:
https://people.cs.clemson.edu/~dhouse/courses/401/notes/affines-matrices.pdf
.
Best,
Kristoffer

Hello,

I am trying to optimize coil positioning and orientation for TMS but I am
not sure how to apply the affine transformation matrix in Localite
(matrix shown below). I used headreco to generate the headmodel.
- Because I used headreco, the values in the matrix are in native space, is
that correct?
- How do I define the entry target in Localite? Would this be 84.3, -8.4,
35.6?
- How do I calculate the rotation angle from this matrix? I am aware of the
coil and axes orientations in SimNIBS and Localite (attached) but do not
know how to use that information to set the rotation angle.

Affine matrix after TMSoptimize:
[[-5.7218e-03 -3.2704e-01 -9.4499e-01  8.4300e+01]
 [-8.5258e-01 -4.9224e-01  1.7551e-01 -8.3755e+00]
 [-5.2256e-01  8.0669e-01 -2.7601e-01  3.5573e+01]
 [ 0.0000e+00  0.0000e+00  0.0000e+00  1.0000e+00]]

Thank you in advance, I appreciate all the help I can get.
Goi Khia

--
Goi Khia Eng
Postdoctoral Fellow, Department of Psychiatry
New York University School of Medicine
Visiting Scientist
Nathan Kline Institute for Psychiatric Research
goikhia.eng at nyulangone.org
goikhia.eng at nki.rfmh.org


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From hensel.lukas at gmail.com  Mon Apr 11 10:07:20 2022
From: hensel.lukas at gmail.com (Lukas Hensel)
Date: Mon, 11 Apr 2022 10:07:20 +0200
Subject: [Simnibs-discuss] Simnibs error - could not find tissue
 probability maps
Message-ID: <2CB4F1DE-5795-45AB-B3D0-28064F09EEA0@gmail.com>

Dear all,

My name is Lukas Hensel and im researching on TMS in stroke in the university hospital in cologne, Germany. Trying to run the headreco, I?m encountering the following error (Command window and headreco_logposted below, System: macOS Catalina V10.15.7). I?m grateful for any ideas how to solve this.

Best
Lukas



###### terminal log:

lukashensel at Lukass-MacBook-Pro 0_2219 % headreco all 0_2219 3D/2219S160810_174718_0006_t1_mprage_0.9mm.nii 3D/2219S160810_175251_0007_t2w_space_0.9mm.nii

========================================================================
PREPARING VOLUMES FOR MESHING
========================================================================

Copying input files to m2m_0_2219

Copying T1fs.nii.gz to T1fs_conform.nii.gz
Preparing to segment

Starting MATLAB
========================================================================
Binarizing tissue probability maps
Traceback (most recent call last):
  File "/Users/lukashensel/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module>
    main()
  File "/Users/lukashensel/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
    headmodel(sys.argv)
  File "/Users/lukashensel/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel
    raise OSError('Could not find tissue probability maps.\n'
OSError: Could not find tissue probability maps.
Probably something went wrong with the Matlab call or SPM
(base) lukashensel at Lukass-MacBook-Pro 0_2219 % 

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From jj3g17 at soton.ac.uk  Thu Apr 14 17:15:24 2022
From: jj3g17 at soton.ac.uk (Jaimie Jobson (jj3g17))
Date: Thu, 14 Apr 2022 15:15:24 +0000
Subject: [Simnibs-discuss] Multiple tDCS simulations employing Lead-field
Message-ID: <LNXP265MB088949AF318A12C9180DBF59DDEF9@LNXP265MB0889.GBRP265.PROD.OUTLOOK.COM>


Hello,

I?m an Msc student working on creating a neural network that is capable of predicting the magnitude of electric field at a given position/positions in the brain (tDCS). For this I?m using a 19 electrode cap. I need to be able to quickly and automatically find the electric field at a given position for a large combination of electrodes and positions. For example to predict the e field at a position created when two electrodes are switched on from the 19 electrode cap. However to accomplish this I need to be able to simulate hundreds if not thousands of combinations (depending on how many electrodes are switched on). Doing this by undertaking thousands of simulation would be extremely time consuming, however from my understanding I could very quickly find the E field at certain positions for many hundreds of electrode combinations by using the Lead-field of a head model. All information related to Lead-fields refers to optimization, however can it be used to predict the outcome of many simulations. If so how would I go about programming this.

Thanks

Jaimie Jobson
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From axelt at drcmr.dk  Fri Apr 15 13:46:06 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Fri, 15 Apr 2022 13:46:06 +0200
Subject: [Simnibs-discuss] Multiple tDCS simulations employing Lead-field
In-Reply-To: <LNXP265MB088949AF318A12C9180DBF59DDEF9@LNXP265MB0889.GBRP265.PROD.OUTLOOK.COM>
References: <LNXP265MB088949AF318A12C9180DBF59DDEF9@LNXP265MB0889.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <9521ae1f-411c-7a26-98c8-29c9c521bc98@drcmr.dk>

Hi,

you can easily calculate the fields created by any combination of 
electrode currents using a linear combination of the lead fields. The 
only constraint is that electrode currents sum up to zero. The 
leadfields are all calcuated relative to a common reference electrode 
for a unit current. The field between, e.g. for a current flow of 2 mA 
between electrodes 1 and 2 is then:

EF(El2 to El1, 2mA) = 2mA*( EF(El2 to El_ref) - EF(El1 to El_ref) ) = 
2mA*(leadfield_El2 - leadfield_El1).

Hope this helps.

Best,

Axel

On 14-04-2022 17:15, Jaimie Jobson (jj3g17) wrote:
>
> Hello,
>
> I?m an Msc student working on creating a neural network that is 
> capable of predicting the magnitude of electric field at a given 
> position/positions in the brain (tDCS). For this I?m using a 19 
> electrode cap. I need to be able to quickly and automatically find the 
> electric field at a given position for a large combination of 
> electrodes and positions. For example to predict the e field at a 
> position created when two electrodes are switched on from the 19 
> electrode cap. However to accomplish this I need to be able to 
> simulate hundreds if not thousands of combinations (depending on how 
> many electrodes are switched on). Doing this by undertaking thousands 
> of simulation would be extremely time consuming, however from my 
> understanding I could very quickly find the E field at certain 
> positions for many hundreds of electrode combinations by using the 
> Lead-field of a head model. All information related to Lead-fields 
> refers to optimization, however can it be used to predict the outcome 
> of many simulations. If so how would I go about programming this.
>
> Thanks
>
> Jaimie Jobson
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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From vesanusx at gmail.com  Sat Apr 16 17:38:00 2022
From: vesanusx at gmail.com (Sauch McFarlane)
Date: Sat, 16 Apr 2022 16:38:00 +0100
Subject: [Simnibs-discuss] Uncertainty Quantification
Message-ID: <CALFED7fKm+ELzpJMHnFsUhpqOZEnC+qT93J0BTwO725oNxeHtw@mail.gmail.com>

Good afternoon,

I hope you're doing well.

I've been looking through your documentation on the Uncertainty
Quantification and I'm having some trouble with the MATLAB code examples
provided on the website (
https://simnibs.github.io/simnibs/build/html/tutorial/advanced/uq.html)

MATLAB throws up an error at the very first line of the script "s =
sim_struct('SESSION');" with the error
 "Undefined function or variable 'sim_struct'.
Error in UncertaintyQALL (line 8)
s = sim_struct('SESSION');"

So far, I've tried with and without a capital S because the different pages
on the website are inconsistent about this, and all other changes I have
attempted have been fruitless. Can you advise on how to fix this error?

Many thanks,
Sauch
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From vesanusx at gmail.com  Mon Apr 18 11:32:09 2022
From: vesanusx at gmail.com (Sauch McFarlane)
Date: Mon, 18 Apr 2022 10:32:09 +0100
Subject: [Simnibs-discuss] Uncertainty Quantification
In-Reply-To: <CALFED7fKm+ELzpJMHnFsUhpqOZEnC+qT93J0BTwO725oNxeHtw@mail.gmail.com>
References: <CALFED7fKm+ELzpJMHnFsUhpqOZEnC+qT93J0BTwO725oNxeHtw@mail.gmail.com>
Message-ID: <CALFED7d9fiaNM23_idhOyJR7_-_hBFXL0AzaNS=h7bnNHetS6A@mail.gmail.com>

Good afternoon,

I hope you're doing well. I'm not sure if this sent correctly the first
time, so I'm re-sending it now.

I've been looking through your documentation on the Uncertainty
Quantification and I'm having some trouble with the MATLAB code examples
provided on the website (
https://simnibs.github.io/simnibs/build/html/tutorial/advanced/uq.html)

MATLAB throws up an error at the very first line of the script "s =
sim_struct('SESSION');" with the error
 "Undefined function or variable 'sim_struct'.
Error in UncertaintyQALL (line 8)
s = sim_struct('SESSION');"

So far, I've tried with and without a capital S because the different pages
on the website are inconsistent about this, and all other changes I have
attempted have been fruitless. Can you advise on how to fix this error?

Many thanks,
Sauch

On Sat, 16 Apr 2022 at 16:38, Sauch McFarlane <vesanusx at gmail.com> wrote:

> Good afternoon,
>
> I hope you're doing well.
>
> I've been looking through your documentation on the Uncertainty
> Quantification and I'm having some trouble with the MATLAB code examples
> provided on the website (
> https://simnibs.github.io/simnibs/build/html/tutorial/advanced/uq.html)
>
> MATLAB throws up an error at the very first line of the script "s =
> sim_struct('SESSION');" with the error
>  "Undefined function or variable 'sim_struct'.
> Error in UncertaintyQALL (line 8)
> s = sim_struct('SESSION');"
>
> So far, I've tried with and without a capital S because the different
> pages on the website are inconsistent about this, and all other changes I
> have attempted have been fruitless. Can you advise on how to fix this error?
>
> Many thanks,
> Sauch
>
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From geh261 at nyu.edu  Fri Apr 15 18:47:54 2022
From: geh261 at nyu.edu (Grace Hallenbeck)
Date: Fri, 15 Apr 2022 12:47:54 -0400
Subject: [Simnibs-discuss] coil positioning in simnibs 3.2.6
Message-ID: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>

Dear simnibs crew,

Hello! My name is Grace Hallenbeck and I'm a post-doc working with Clay
Curtis (cc'ed here) at NYU. We're interested in using simnibs to model the
effects of TMS and today we've been trying to correctly position the coil
orientation in the simnibs gui but are having some difficulty.

We have a coordinate of interest that we're plugging in for the x,y,z
'Position' fields. But we're unclear on the best way to work with the
'Direction Reference' coordinates, which is what we think controls the coil
orientation. In the screenshot below, I've plugged in the same x,y,z coords
as in 'Position', but this has the coil handle (as I understand, 180 deg
opposite the green line) pointing slightly off the coil orientation we
actually applied TMS at with this subject (what we are attempting to
model).

So our question is: how can we finely modulate the coil orientation,
keeping the 'Position' x,y,z coords constant? We would greatly appreciate
any help on this as we're getting a publication ready and hope to include
some modeling results.
[image: Screen Shot 2022-04-15 at 12.32.29 PM.png]

All the best & thanks for your work,

Grace Hallenbeck
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From clayton.curtis at nyu.edu  Fri Apr 15 19:12:59 2022
From: clayton.curtis at nyu.edu (Clayton E Curtis)
Date: Fri, 15 Apr 2022 13:12:59 -0400
Subject: [Simnibs-discuss] coil positioning in simnibs 3.2.6
In-Reply-To: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>
References: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>
Message-ID: <CAG0H7ccyxwTRkhmMCnB=feptwx0DBHAnqnR7OgXOTQQi8u6i6Q@mail.gmail.com>

Hi,

I just wanted to add a couple of details here.  We are using Brainsight to
acquire the Coil Position, and that looks spot on. But we are interested in
correctly orienting the coil before running the model. The documentation
was rather sparse here.

Also, Grace is alluding the fact that when we make changes to the Reference
Coordinates, it makes changes to the Coil Position.  Not sure what this is
about?

Thanks for your help!

/cc

On Fri, Apr 15, 2022 at 12:48 PM Grace Hallenbeck <geh261 at nyu.edu> wrote:

> Dear simnibs crew,
>
> Hello! My name is Grace Hallenbeck and I'm a post-doc working with Clay
> Curtis (cc'ed here) at NYU. We're interested in using simnibs to model the
> effects of TMS and today we've been trying to correctly position the coil
> orientation in the simnibs gui but are having some difficulty.
>
> We have a coordinate of interest that we're plugging in for the x,y,z
> 'Position' fields. But we're unclear on the best way to work with the
> 'Direction Reference' coordinates, which is what we think controls the coil
> orientation. In the screenshot below, I've plugged in the same x,y,z coords
> as in 'Position', but this has the coil handle (as I understand, 180 deg
> opposite the green line) pointing slightly off the coil orientation we
> actually applied TMS at with this subject (what we are attempting to
> model).
>
> So our question is: how can we finely modulate the coil orientation,
> keeping the 'Position' x,y,z coords constant? We would greatly appreciate
> any help on this as we're getting a publication ready and hope to include
> some modeling results.
> [image: Screen Shot 2022-04-15 at 12.32.29 PM.png]
>
> All the best & thanks for your work,
>
> Grace Hallenbeck
>
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From axelt at drcmr.dk  Mon Apr 18 11:50:49 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Mon, 18 Apr 2022 11:50:49 +0200
Subject: [Simnibs-discuss] Uncertainty Quantification
In-Reply-To: <CALFED7d9fiaNM23_idhOyJR7_-_hBFXL0AzaNS=h7bnNHetS6A@mail.gmail.com>
References: <CALFED7fKm+ELzpJMHnFsUhpqOZEnC+qT93J0BTwO725oNxeHtw@mail.gmail.com>
 <CALFED7d9fiaNM23_idhOyJR7_-_hBFXL0AzaNS=h7bnNHetS6A@mail.gmail.com>
Message-ID: <59c097fc-a25a-e081-adf1-243e261cc53e@drcmr.dk>

Hi,

did you add the simnibs matlab functions to your Matlab search path?

There's a "matlab" subfolder in the simnibs installation directory which 
you need to add. You can try typing "mesh_save_gmsh4", if that is also 
not found, then the missing search path is likely the reason.

Best,

Axel


On 18-04-2022 11:32, Sauch McFarlane wrote:
> Good afternoon,
>
> I hope you're doing well. I'm not sure if this sent correctly the 
> first time, so I'm re-sending it now.
>
> I've been looking through your documentation on the Uncertainty 
> Quantification and I'm having some trouble with the MATLAB code 
> examples provided on the?website 
> (https://simnibs.github.io/simnibs/build/html/tutorial/advanced/uq.html)
>
> MATLAB throws up an error at the very first line of the script "s = 
> sim_struct('SESSION');" with the error
> ?"Undefined function or variable 'sim_struct'.
> Error in UncertaintyQALL (line 8)
> s = sim_struct('SESSION');"
>
> So far, I've tried with and without a capital S because the different 
> pages on the website are inconsistent about this, and all other 
> changes I have attempted have been fruitless. Can you advise on how to 
> fix this error?
>
> Many thanks,
> Sauch
>
> On Sat, 16 Apr 2022 at 16:38, Sauch McFarlane <vesanusx at gmail.com> wrote:
>
>     Good afternoon,
>
>     I hope you're doing well.
>
>     I've been looking through your documentation on the Uncertainty
>     Quantification and I'm having some trouble with the MATLAB code
>     examples provided on the?website
>     (https://simnibs.github.io/simnibs/build/html/tutorial/advanced/uq.html)
>
>     MATLAB throws up an error at the very first line of the script "s
>     = sim_struct('SESSION');" with the error
>     ?"Undefined function or variable 'sim_struct'.
>     Error in UncertaintyQALL (line 8)
>     s = sim_struct('SESSION');"
>
>     So far, I've tried with and without a capital S because the
>     different pages on the website are inconsistent about this, and
>     all other changes I have attempted have been fruitless. Can you
>     advise on how to fix this error?
>
>     Many thanks,
>     Sauch
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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From Ben.Hatton at nottingham.ac.uk  Mon Apr 25 14:52:36 2022
From: Ben.Hatton at nottingham.ac.uk (Ben Hatton)
Date: Mon, 25 Apr 2022 12:52:36 +0000
Subject: [Simnibs-discuss] "Gmsh failed meshing one or more surfaces. Trying
	Delaunay meshing"
Message-ID: <PR3PR06MB6683A0757EB125D42A3468E49AF89@PR3PR06MB6683.eurprd06.prod.outlook.com>

Hi,

I am using the ernie data set to try out headreco, and have found that there is gmsh error when meshing. I ran the file on a compute cluster using linux, and have installed simnibs with anaconda.

Here is the error message:

GENERATING VOLUME MESH
========================================================================
Creating .geo file
Creating volume mesh using Gmsh
========================================================================
Gmsh exit code: 127
Gmsh failed meshing one or more surfaces. Doing uniform remeshing and retrying
Remeshing wm.stl
Remeshing gm.stl
Remeshing csf.stl
Remeshing bone.stl
Remeshing skin.stl
Remeshing eyes.stl
Remeshing cavities.stl
Remeshing air_outer_decoupled.stl
Remeshing ventricles.stl
Decoupling
Decoupling ventricles from GM
Decoupling WM from ventricles
Decoupling GM from WM
Gmsh exit code: 127
Gmsh failed meshing one or more surfaces. Trying Delaunay meshing
Gmsh exit code: 127

Traceback (most recent call last):
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module>
    sys.exit(main())
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
    headmodel(sys.argv)
 File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel
    vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh
    raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))
RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.



And the log is here:

2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl
2022-04-25 13:05:31 [DEBUG] Testing for intersections ...
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:06:07 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl
2022-04-25 13:06:07 [DEBUG] Testing for intersections ...
2022-04-25 13:06:07 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/gmsh" -3 -bin -o "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.msh" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.geo" >> gmsh_log.txt
2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127
2022-04-25 13:06:07 [INFO ] Gmsh failed meshing one or more surfaces. Trying Delaunay meshing
2022-04-25 13:06:07 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/gmsh" -3 -bin -o "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.msh" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.geo" >> gmsh_log.txt
2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127
2022-04-25 13:06:07 [ERROR] Traceback (most recent call last):
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module>
    sys.exit(main())
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
    headmodel(sys.argv)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel
    vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh
    raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))
RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.


Thanks for your help,
Ben



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From geh261 at nyu.edu  Mon Apr 25 21:37:12 2022
From: geh261 at nyu.edu (Grace Hallenbeck)
Date: Mon, 25 Apr 2022 15:37:12 -0400
Subject: [Simnibs-discuss] coil positioning in simnibs 3.2.6
In-Reply-To: <460006303.667477.1650363374296.JavaMail.zimbra@hsancamillo.it>
References: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>
 <CAG0H7ccyxwTRkhmMCnB=feptwx0DBHAnqnR7OgXOTQQi8u6i6Q@mail.gmail.com>
 <460006303.667477.1650363374296.JavaMail.zimbra@hsancamillo.it>
Message-ID: <CAB2vMnG6mVr93DD1S6xxZS+Vr6TZ40MF0jOcDq1bk0D+jxvxXA@mail.gmail.com>

Hi Annalisa,

Thanks for your reply. We have made progress on the translation matrix
cited above, but currently we have a more pressing question.

The file output from a successful headreco, T1fs_conform.nii, appears to be
identical to our input T1, though from the simnibs website, "The head
meshing procedures create a NifTI file called m2m_*subID*
/T1fs_conform.nii.gz. This file contains a transformed T1 image of the
subject, with the world coordinates used by SimNIBS."

However, the voxel orientations and resolutions are identical (per 3dinfo
from afni), with one exception: the template space of the conform file is
TLRC while that of the original T1 is ORIG. So, my questions are the
following:

1. Should these files be identical?
2. Why is the template space of the conform file TLRC?

copy/pasting header info here for clarity:

INPUT T1

(base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
grace> 3dinfo T1.nii

++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug  6 2016) [64-bit]


Dataset File:    T1.nii

Identifier Code: NII_Hd_qtnnMonBYdt6jsb2XWw  Creation Date: Fri Aug 31
11:14:18 2018

Template Space:  ORIG

Dataset Type:    Anat Bucket (-abuc)

Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]

Storage Mode:    NIFTI

Storage Space:   32,768,000 (33 million [mega]) bytes

Geometry String:
"MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"

Data Axes Tilt:  Plumb

Data Axes Orientation:

  first  (x) = Right-to-Left

  second (y) = Superior-to-Inferior

  third  (z) = Posterior-to-Anterior   [-orient RSP]

R-to-L extent:  -128.100 [R] -to-   127.100 [L] -step-     0.800 mm [320
voxels]

A-to-P extent:  -127.100 [A] -to-   128.100 [P] -step-     0.800 mm [320
voxels]

I-to-S extent:  -127.100 [I] -to-   128.100 [S] -step-     0.800 mm [320
voxels]

Number of values stored at each pixel = 1

  -- At sub-brick #0 '?' datum type is byte:            0 to           255

T1fs_conform

(base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
grace> 3dinfo T1fs_conform.nii

++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug  6 2016) [64-bit]

** AFNI converts NIFTI_datatype=512 (UINT16) in file T1fs_conform.nii to
FLOAT32

     Warnings of this type will be muted for this session.

     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.


Dataset File:    T1fs_conform.nii

Identifier Code: NII_BDbiP8aLlBK7bpodSIpPwA  Creation Date: Mon Apr 25
15:30:40 2022

Template Space:  TLRC

Dataset Type:    Anat Bucket (-abuc)

Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]

Storage Mode:    NIFTI

Storage Space:   131,072,000 (131 million [mega]) bytes

Geometry String:
"MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"

Data Axes Tilt:  Plumb

Data Axes Orientation:

  first  (x) = Right-to-Left

  second (y) = Superior-to-Inferior

  third  (z) = Posterior-to-Anterior   [-orient RSP]

R-to-L extent:  -128.100 [R] -to-   127.100 [L] -step-     0.800 mm [320
voxels]

A-to-P extent:  -127.100 [A] -to-   128.100 [P] -step-     0.800 mm [320
voxels]

I-to-S extent:  -127.100 [I] -to-   128.100 [S] -step-     0.800 mm [320
voxels]

Number of values stored at each pixel = 1

  -- At sub-brick #0 '?' datum type is float

Thanks very much for your help!

Sincerely,

Grace

On Tue, Apr 19, 2022 at 6:16 AM Annalisa Schuler <
annalisa.schuler at hsancamillo.it> wrote:

> Dear all,
>
> are you using neuronavigation for your project, if yes you should get a
> matrix including coil position, translation and orientation from your
> stimulation session, which allows you to calculate exact positions using
> matsimnibs (
> https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__simnibs.github.io_simnibs_build_html_documentation_sim-5Fstruct_position.html&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=hlYoGF-M-jRATsmPq_apB2jsYCrtnhaxmOo1DPoxuno&e=>
> ).
>
> All the best,
>
> AL
>
> *Annalisa Schuler*
> Ricercatrice Psicologa
> _______________________________________________
> *SAN CAMILLO IRCCS S.R.L. societ? unipersonale*
> soggetta a direzione e coordinamento da parte della
> Fondazione Villa Salus
> Via Alberoni, 70 - 30126 Venezia - Lido
> P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3
>
>
> *Certificazione UNI EN ISO 9001:2015* Certificato SGQ 5010016444 emesso
> da TUV SUD Italia
>
> *Laboratorio di Imaging Clinico e Stimolazione*
>
> Sito web
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=n7WrKbPtiB6T0x_y37Fmp6LflxWHPketwsV8lhgBvnc&e=>
>  | Facebook
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=8yayA4Zr6-zDVlz5EXiQU6dbWv8kwh2opI5qhf6nQ4A&e=>
>  | Linkedin
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_san-2Dcamillo-2Dirccs&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZSfKGfVvtq97KLPP2EEhBcCTZI3HlBavqLi2mkM0Zw&e=>
>  | Twitter
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=81zmg2aVNdMorLXTwO7exfqWC_MIwZiGlqWOBdx40c0&e=> |
> Instagram
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.instagram.com_irccssancamillo_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZqznf8r5k9Gxtz2IU0Cc0DEBhVgeKeGiE6B4SO2p_0&e=>
> [image: San Camillo IRCCS]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=CIYDpmlDD17OMI-6_fbAAXJJrT1lO7mpXWEoum-BN8I&e=>
>
> [image: 5x1000 al San Camillo Onlus]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_5x1000&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=wBw6kgoykSkkYXdHiOIBs_hvP1kQL0rnA1sqinrb5oQ&e=>
>
> ------------------------------
> *Da: *"Clayton E Curtis" <clayton.curtis at nyu.edu>
> *A: *"Grace Hallenbeck" <geh261 at nyu.edu>
> *Cc: *"discuss at simnibs.org" <discuss at simnibs.org>
> *Inviato: *Venerd?, 15 aprile 2022 19:12:59
> *Oggetto: *Re: [Simnibs-discuss] coil positioning in simnibs 3.2.6
>
> Hi,
> I just wanted to add a couple of details here.  We are using Brainsight to
> acquire the Coil Position, and that looks spot on. But we are interested in
> correctly orienting the coil before running the model. The documentation
> was rather sparse here.
>
> Also, Grace is alluding the fact that when we make changes to the
> Reference Coordinates, it makes changes to the Coil Position.  Not sure
> what this is about?
>
> Thanks for your help!
>
> /cc
>
> On Fri, Apr 15, 2022 at 12:48 PM Grace Hallenbeck <geh261 at nyu.edu> wrote:
>
>> Dear simnibs crew,
>> Hello! My name is Grace Hallenbeck and I'm a post-doc working with Clay
>> Curtis (cc'ed here) at NYU. We're interested in using simnibs to model the
>> effects of TMS and today we've been trying to correctly position the coil
>> orientation in the simnibs gui but are having some difficulty.
>>
>> We have a coordinate of interest that we're plugging in for the x,y,z
>> 'Position' fields. But we're unclear on the best way to work with the
>> 'Direction Reference' coordinates, which is what we think controls the coil
>> orientation. In the screenshot below, I've plugged in the same x,y,z coords
>> as in 'Position', but this has the coil handle (as I understand, 180 deg
>> opposite the green line) pointing slightly off the coil orientation we
>> actually applied TMS at with this subject (what we are attempting to
>> model).
>>
>> So our question is: how can we finely modulate the coil orientation,
>> keeping the 'Position' x,y,z coords constant? We would greatly appreciate
>> any help on this as we're getting a publication ready and hope to include
>> some modeling results.
>> [image: Screen Shot 2022-04-15 at 12.32.29 PM.png]
>>
>> All the best & thanks for your work,
>> Grace Hallenbeck
>>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From axelt at drcmr.dk  Tue Apr 26 10:11:40 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 26 Apr 2022 10:11:40 +0200
Subject: [Simnibs-discuss] coil positioning in simnibs 3.2.6
In-Reply-To: <CAB2vMnG6mVr93DD1S6xxZS+Vr6TZ40MF0jOcDq1bk0D+jxvxXA@mail.gmail.com>
References: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>
 <CAG0H7ccyxwTRkhmMCnB=feptwx0DBHAnqnR7OgXOTQQi8u6i6Q@mail.gmail.com>
 <460006303.667477.1650363374296.JavaMail.zimbra@hsancamillo.it>
 <CAB2vMnG6mVr93DD1S6xxZS+Vr6TZ40MF0jOcDq1bk0D+jxvxXA@mail.gmail.com>
Message-ID: <17f5aac3-5572-9ef5-8649-ca7a8e559b56@drcmr.dk>

Hi Grace,

the two files are indeed identical, unless you specify something else 
using the -d option.

The qform and sform of the T1fs_conform just are set to the same, which 
then likely causes AFNI to select TLRC.

Best regards,

Axel


On 25-04-2022 21:37, Grace Hallenbeck wrote:
> Hi Annalisa,
>
> Thanks for your reply. We have made progress on the translation matrix 
> cited above, but currently we have a more pressing question.
>
> The file output from a successful?headreco, T1fs_conform.nii, appears 
> to be identical to our input T1, though from the simnibs website, "The 
> head meshing procedures create a NifTI file called 
> |m2m_||/subID/||/T1fs_conform.nii.gz|. This file contains a 
> transformed T1 image of the subject, with the world coordinates used 
> by SimNIBS."
>
> However, the voxel orientations and resolutions are identical (per 
> 3dinfo from afni), with one exception: the template space of the 
> conform file is TLRC while that of the original T1 is ORIG. So, my 
> questions are the following:
>
> 1. Should these files be identical?
> 2. Why is the template space of the conform file TLRC?
>
> copy/pasting header info here for clarity:
>
> INPUT T1
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes 
> grace> 3dinfo T1.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug6 2016) [64-bit]
>
>
> Dataset File:T1.nii
>
> Identifier Code: NII_Hd_qtnnMonBYdt6jsb2XWwCreation Date: Fri Aug 31 
> 11:14:18 2018
>
> Template Space:ORIG
>
> Dataset Type:Anat Bucket (-abuc)
>
> Byte Order:LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode:NIFTI
>
> Storage Space: 32,768,000 (33 million [mega]) bytes
>
> Geometry String: 
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt:Plumb
>
> Data Axes Orientation:
>
> first(x) = Right-to-Left
>
> second (y) = Superior-to-Inferior
>
> third(z) = Posterior-to-Anterior [-orient RSP]
>
> R-to-L extent:-128.100 [R] -to- 127.100 [L] -step- 0.800 mm [320 voxels]
>
> A-to-P extent:-127.100 [A] -to- 128.100 [P] -step- 0.800 mm [320 voxels]
>
> I-to-S extent:-127.100 [I] -to- 128.100 [S] -step- 0.800 mm [320 voxels]
>
> Number of values stored at each pixel = 1
>
> -- At sub-brick #0 '?' datum type is byte:0 to 255
>
>
> T1fs_conform
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes 
> grace> 3dinfo T1fs_conform.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug6 2016) [64-bit]
>
> ** AFNI converts NIFTI_datatype=512 (UINT16) in file T1fs_conform.nii 
> to FLOAT32
>
> Warnings of this type will be muted for this session.
>
> Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
>
>
> Dataset File:T1fs_conform.nii
>
> Identifier Code: NII_BDbiP8aLlBK7bpodSIpPwACreation Date: Mon Apr 25 
> 15:30:40 2022
>
> Template Space:TLRC
>
> Dataset Type:Anat Bucket (-abuc)
>
> Byte Order:LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode:NIFTI
>
> Storage Space: 131,072,000 (131 million [mega]) bytes
>
> Geometry String: 
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt:Plumb
>
> Data Axes Orientation:
>
> first(x) = Right-to-Left
>
> second (y) = Superior-to-Inferior
>
> third(z) = Posterior-to-Anterior [-orient RSP]
>
> R-to-L extent:-128.100 [R] -to- 127.100 [L] -step- 0.800 mm [320 voxels]
>
> A-to-P extent:-127.100 [A] -to- 128.100 [P] -step- 0.800 mm [320 voxels]
>
> I-to-S extent:-127.100 [I] -to- 128.100 [S] -step- 0.800 mm [320 voxels]
>
> Number of values stored at each pixel = 1
>
> -- At sub-brick #0 '?' datum type is float
>
>
> Thanks very much for your help!
>
> Sincerely,
>
> Grace
>
> On Tue, Apr 19, 2022 at 6:16 AM Annalisa Schuler 
> <annalisa.schuler at hsancamillo.it> wrote:
>
>     Dear all,
>
>     are you using neuronavigation for your project, if yes you should
>     get a matrix including coil position, translation and orientation
>     from your stimulation session, which allows you to calculate exact
>     positions using matsimnibs
>     (https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__simnibs.github.io_simnibs_build_html_documentation_sim-5Fstruct_position.html&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=hlYoGF-M-jRATsmPq_apB2jsYCrtnhaxmOo1DPoxuno&e=>).
>
>     All the best,
>
>     AL
>
>     *Annalisa Schuler*
>     Ricercatrice Psicologa
>     _______________________________________________
>     *SAN CAMILLO IRCCS S.R.L. societ? unipersonale*
>     soggetta a direzione e coordinamento da parte della
>     Fondazione Villa Salus
>     Via Alberoni, 70 - 30126 Venezia - Lido
>     P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3
>
>     *Certificazione UNI EN ISO 9001:2015
>     * Certificato SGQ 5010016444 emesso da TUV SUD Italia
>
>     *Laboratorio di Imaging Clinico e Stimolazione*
>
>     Sito web
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=n7WrKbPtiB6T0x_y37Fmp6LflxWHPketwsV8lhgBvnc&e=>?|
>     Facebook
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=8yayA4Zr6-zDVlz5EXiQU6dbWv8kwh2opI5qhf6nQ4A&e=>?|
>     Linkedin
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_san-2Dcamillo-2Dirccs&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZSfKGfVvtq97KLPP2EEhBcCTZI3HlBavqLi2mkM0Zw&e=>?|
>     Twitter
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=81zmg2aVNdMorLXTwO7exfqWC_MIwZiGlqWOBdx40c0&e=>?|
>     Instagram
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.instagram.com_irccssancamillo_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZqznf8r5k9Gxtz2IU0Cc0DEBhVgeKeGiE6B4SO2p_0&e=>
>
>     San Camillo IRCCS
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=CIYDpmlDD17OMI-6_fbAAXJJrT1lO7mpXWEoum-BN8I&e=>
>
>
>     5x1000 al San Camillo Onlus
>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_5x1000&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=wBw6kgoykSkkYXdHiOIBs_hvP1kQL0rnA1sqinrb5oQ&e=>
>
>
>     ------------------------------------------------------------------------
>     *Da: *"Clayton E Curtis" <clayton.curtis at nyu.edu>
>     *A: *"Grace Hallenbeck" <geh261 at nyu.edu>
>     *Cc: *"discuss at simnibs.org" <discuss at simnibs.org>
>     *Inviato: *Venerd?, 15 aprile 2022 19:12:59
>     *Oggetto: *Re: [Simnibs-discuss] coil positioning in simnibs 3.2.6
>
>     Hi,
>     I just wanted to add a couple of details here. We are using
>     Brainsight to acquire the Coil Position, and that looks spot
>     on.?But we are interested in correctly orienting the coil before
>     running the model. The documentation was rather sparse here.
>
>     Also, Grace is alluding the fact that when we make changes to the
>     Reference Coordinates, it makes changes to the Coil Position.? Not
>     sure what this is about?
>
>     Thanks for your help!
>
>     /cc
>
>     On Fri, Apr 15, 2022 at 12:48 PM Grace Hallenbeck <geh261 at nyu.edu>
>     wrote:
>
>         Dear simnibs crew,
>         Hello! My name is Grace Hallenbeck and I'm a post-doc working
>         with Clay Curtis (cc'ed?here) at NYU.?We're interested in
>         using simnibs to model the effects of TMS and today?we've been
>         trying to correctly position the coil orientation in the
>         simnibs gui but are having some difficulty.
>
>         We have a coordinate of interest that we're plugging in for
>         the x,y,z 'Position' fields. But we're unclear on the best way
>         to work with the 'Direction Reference' coordinates,?which is
>         what we think controls the coil orientation. In the screenshot
>         below, I've plugged in the same x,y,z coords as in 'Position',
>         but this has the coil handle (as I understand, 180 deg
>         opposite the green line) pointing slightly off the coil
>         orientation we actually applied TMS at with this subject (what
>         we are attempting to model).
>
>         So our question is: how can we finely modulate?the coil
>         orientation, keeping the 'Position' x,y,z coords constant? We
>         would greatly appreciate any help on this as we're getting a
>         publication ready and hope to include some modeling results.
>         Screen Shot 2022-04-15 at 12.32.29 PM.png
>
>         All the best & thanks for your work,
>         Grace Hallenbeck
>
>
>     _______________________________________________
>     Simnibs-discuss mailing list
>     Simnibs-discuss at drcmr.dk
>     https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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From geh261 at nyu.edu  Tue Apr 26 17:21:39 2022
From: geh261 at nyu.edu (Grace Hallenbeck)
Date: Tue, 26 Apr 2022 11:21:39 -0400
Subject: [Simnibs-discuss] coil positioning in simnibs 3.2.6
In-Reply-To: <17f5aac3-5572-9ef5-8649-ca7a8e559b56@drcmr.dk>
References: <CAB2vMnFOGVr7P9EuSaWBqPA6eWgkgTOZq0kvXJ-=Kuaue=f3WQ@mail.gmail.com>
 <CAG0H7ccyxwTRkhmMCnB=feptwx0DBHAnqnR7OgXOTQQi8u6i6Q@mail.gmail.com>
 <460006303.667477.1650363374296.JavaMail.zimbra@hsancamillo.it>
 <CAB2vMnG6mVr93DD1S6xxZS+Vr6TZ40MF0jOcDq1bk0D+jxvxXA@mail.gmail.com>
 <17f5aac3-5572-9ef5-8649-ca7a8e559b56@drcmr.dk>
Message-ID: <CAB2vMnEGGbseQfsEvDYn_2uez3OVgwOD0PmgfkGfS+urXtc6+w@mail.gmail.com>

Hi Axel,

Wonderful!! Thank you so very much for confirming this. We are working on
setting up a protocol and instructions for younger lab members on how to
use simnibs and I can now include a note about this. We thank you immensely
for not only answering the above q, but for all of the work you and the
team have put in to bring simnibs to the world.

Cheers!

Grace

On Tue, Apr 26, 2022 at 4:11 AM Axel Thielscher <axelt at drcmr.dk> wrote:

> Hi Grace,
>
> the two files are indeed identical, unless you specify something else
> using the -d option.
>
> The qform and sform of the T1fs_conform just are set to the same, which
> then likely causes AFNI to select TLRC.
>
> Best regards,
>
> Axel
>
>
> On 25-04-2022 21:37, Grace Hallenbeck wrote:
>
> Hi Annalisa,
>
> Thanks for your reply. We have made progress on the translation matrix
> cited above, but currently we have a more pressing question.
>
> The file output from a successful headreco, T1fs_conform.nii, appears to
> be identical to our input T1, though from the simnibs website, "The head
> meshing procedures create a NifTI file called m2m_*subID*
> /T1fs_conform.nii.gz. This file contains a transformed T1 image of the
> subject, with the world coordinates used by SimNIBS."
>
> However, the voxel orientations and resolutions are identical (per 3dinfo
> from afni), with one exception: the template space of the conform file is
> TLRC while that of the original T1 is ORIG. So, my questions are the
> following:
>
> 1. Should these files be identical?
> 2. Why is the template space of the conform file TLRC?
>
> copy/pasting header info here for clarity:
>
> INPUT T1
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
> grace> 3dinfo T1.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug  6 2016) [64-bit]
>
>
> Dataset File:    T1.nii
>
> Identifier Code: NII_Hd_qtnnMonBYdt6jsb2XWw  Creation Date: Fri Aug 31
> 11:14:18 2018
>
> Template Space:  ORIG
>
> Dataset Type:    Anat Bucket (-abuc)
>
> Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode:    NIFTI
>
> Storage Space:   32,768,000 (33 million [mega]) bytes
>
> Geometry String:
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt:  Plumb
>
> Data Axes Orientation:
>
>   first  (x) = Right-to-Left
>
>   second (y) = Superior-to-Inferior
>
>   third  (z) = Posterior-to-Anterior   [-orient RSP]
>
> R-to-L extent:  -128.100 [R] -to-   127.100 [L] -step-     0.800 mm [320
> voxels]
>
> A-to-P extent:  -127.100 [A] -to-   128.100 [P] -step-     0.800 mm [320
> voxels]
>
> I-to-S extent:  -127.100 [I] -to-   128.100 [S] -step-     0.800 mm [320
> voxels]
>
> Number of values stored at each pixel = 1
>
>   -- At sub-brick #0 '?' datum type is byte:            0 to           255
>
> T1fs_conform
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
> grace> 3dinfo T1fs_conform.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug  6 2016) [64-bit]
>
> ** AFNI converts NIFTI_datatype=512 (UINT16) in file T1fs_conform.nii to
> FLOAT32
>
>      Warnings of this type will be muted for this session.
>
>      Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
>
>
> Dataset File:    T1fs_conform.nii
>
> Identifier Code: NII_BDbiP8aLlBK7bpodSIpPwA  Creation Date: Mon Apr 25
> 15:30:40 2022
>
> Template Space:  TLRC
>
> Dataset Type:    Anat Bucket (-abuc)
>
> Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode:    NIFTI
>
> Storage Space:   131,072,000 (131 million [mega]) bytes
>
> Geometry String:
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt:  Plumb
>
> Data Axes Orientation:
>
>   first  (x) = Right-to-Left
>
>   second (y) = Superior-to-Inferior
>
>   third  (z) = Posterior-to-Anterior   [-orient RSP]
>
> R-to-L extent:  -128.100 [R] -to-   127.100 [L] -step-     0.800 mm [320
> voxels]
>
> A-to-P extent:  -127.100 [A] -to-   128.100 [P] -step-     0.800 mm [320
> voxels]
>
> I-to-S extent:  -127.100 [I] -to-   128.100 [S] -step-     0.800 mm [320
> voxels]
>
> Number of values stored at each pixel = 1
>
>   -- At sub-brick #0 '?' datum type is float
>
> Thanks very much for your help!
>
> Sincerely,
>
> Grace
>
> On Tue, Apr 19, 2022 at 6:16 AM Annalisa Schuler <
> annalisa.schuler at hsancamillo.it> wrote:
>
>> Dear all,
>>
>> are you using neuronavigation for your project, if yes you should get a
>> matrix including coil position, translation and orientation from your
>> stimulation session, which allows you to calculate exact positions using
>> matsimnibs (
>> https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__simnibs.github.io_simnibs_build_html_documentation_sim-5Fstruct_position.html&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=hlYoGF-M-jRATsmPq_apB2jsYCrtnhaxmOo1DPoxuno&e=>
>> ).
>>
>> All the best,
>>
>> AL
>>
>> *Annalisa Schuler*
>> Ricercatrice Psicologa
>> _______________________________________________
>> *SAN CAMILLO IRCCS S.R.L. societ? unipersonale*
>> soggetta a direzione e coordinamento da parte della
>> Fondazione Villa Salus
>> Via Alberoni, 70 - 30126 Venezia - Lido
>> P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3
>>
>>
>> *Certificazione UNI EN ISO 9001:2015 * Certificato SGQ 5010016444 emesso
>> da TUV SUD Italia
>>
>> *Laboratorio di Imaging Clinico e Stimolazione*
>>
>> Sito web
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=n7WrKbPtiB6T0x_y37Fmp6LflxWHPketwsV8lhgBvnc&e=>
>>  | Facebook
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=8yayA4Zr6-zDVlz5EXiQU6dbWv8kwh2opI5qhf6nQ4A&e=>
>>  | Linkedin
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_san-2Dcamillo-2Dirccs&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZSfKGfVvtq97KLPP2EEhBcCTZI3HlBavqLi2mkM0Zw&e=>
>>  | Twitter
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=81zmg2aVNdMorLXTwO7exfqWC_MIwZiGlqWOBdx40c0&e=> |
>> Instagram
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.instagram.com_irccssancamillo_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZqznf8r5k9Gxtz2IU0Cc0DEBhVgeKeGiE6B4SO2p_0&e=>
>> [image: San Camillo IRCCS]
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=CIYDpmlDD17OMI-6_fbAAXJJrT1lO7mpXWEoum-BN8I&e=>
>>
>> [image: 5x1000 al San Camillo Onlus]
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_5x1000&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=wBw6kgoykSkkYXdHiOIBs_hvP1kQL0rnA1sqinrb5oQ&e=>
>>
>> ------------------------------
>> *Da: *"Clayton E Curtis" <clayton.curtis at nyu.edu>
>> *A: *"Grace Hallenbeck" <geh261 at nyu.edu>
>> *Cc: *"discuss at simnibs.org" <discuss at simnibs.org>
>> *Inviato: *Venerd?, 15 aprile 2022 19:12:59
>> *Oggetto: *Re: [Simnibs-discuss] coil positioning in simnibs 3.2.6
>>
>> Hi,
>> I just wanted to add a couple of details here.  We are using Brainsight
>> to acquire the Coil Position, and that looks spot on. But we are interested
>> in correctly orienting the coil before running the model. The documentation
>> was rather sparse here.
>>
>> Also, Grace is alluding the fact that when we make changes to the
>> Reference Coordinates, it makes changes to the Coil Position.  Not sure
>> what this is about?
>>
>> Thanks for your help!
>>
>> /cc
>>
>> On Fri, Apr 15, 2022 at 12:48 PM Grace Hallenbeck <geh261 at nyu.edu> wrote:
>>
>>> Dear simnibs crew,
>>> Hello! My name is Grace Hallenbeck and I'm a post-doc working with Clay
>>> Curtis (cc'ed here) at NYU. We're interested in using simnibs to model the
>>> effects of TMS and today we've been trying to correctly position the coil
>>> orientation in the simnibs gui but are having some difficulty.
>>>
>>> We have a coordinate of interest that we're plugging in for the x,y,z
>>> 'Position' fields. But we're unclear on the best way to work with the
>>> 'Direction Reference' coordinates, which is what we think controls the coil
>>> orientation. In the screenshot below, I've plugged in the same x,y,z coords
>>> as in 'Position', but this has the coil handle (as I understand, 180 deg
>>> opposite the green line) pointing slightly off the coil orientation we
>>> actually applied TMS at with this subject (what we are attempting to
>>> model).
>>>
>>> So our question is: how can we finely modulate the coil orientation,
>>> keeping the 'Position' x,y,z coords constant? We would greatly appreciate
>>> any help on this as we're getting a publication ready and hope to include
>>> some modeling results.
>>> [image: Screen Shot 2022-04-15 at 12.32.29 PM.png]
>>>
>>> All the best & thanks for your work,
>>> Grace Hallenbeck
>>>
>>
>> _______________________________________________
>> Simnibs-discuss mailing list
>> Simnibs-discuss at drcmr.dk
>> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.drcmr.dk_mailman_listinfo_simnibs-2Ddiscuss&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=KAH5UaWKhHK6O-_kvXWhmw6pE88SJ4H7rAMP2A_EwbE&e=>
>>
>
> _______________________________________________
> Simnibs-discuss mailing listSimnibs-discuss at drcmr.dkhttps://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss <https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.drcmr.dk_mailman_listinfo_simnibs-2Ddiscuss&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=KAH5UaWKhHK6O-_kvXWhmw6pE88SJ4H7rAMP2A_EwbE&e=>
>
> --
> Dr. Axel Thielscher
> Professor of Neurophysics and Neuroimaging
> Danish Research Center for Magnetic Resonance
> Copenhagen University Hospital Hvidovre
> DK-2650 Hvidovre, Denmarkwww.drcmr.dk <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.drcmr.dk&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=y-8OqGfp5QNYyd4Z-vICXp4-YKY5U5G0nPHvB2FWBdc&e=>
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngbyhttp://www.healthtech.dtu.dk/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.healthtech.dtu.dk_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=0__DQITmG8VYJwqHpTIbjBxmsjxxXgoPyEWPfVlWG6s&e=>
>
>
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From bellabingbing.zhang at connect.polyu.hk  Wed Apr 27 18:16:14 2022
From: bellabingbing.zhang at connect.polyu.hk (ZHANG, bellabingbing [Student])
Date: Wed, 27 Apr 2022 16:16:14 +0000
Subject: [Simnibs-discuss] SimNIBS Installation
Message-ID: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>

Dear Madam or Sir,

Thanks for shareing SimNIBS , a such wonderful software to public.

I am Bingbing, a Ph.D student from The Hong Kong Polytechnic University.

I am trying to use SimNIBS simulate the E-fields distribution for TMS stimulation. When I try to install the SimNIBS to the Ubuntu Linux, it always failed.
My path did not contain Chinese characters.

Could you give me some suggestions where I am wrong?

Best Regards,
Bingbing

[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.
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From kristofferm at drcmr.dk  Fri Apr 29 12:52:57 2022
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Fri, 29 Apr 2022 12:52:57 +0200
Subject: [Simnibs-discuss] SimNIBS Installation
In-Reply-To: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
References: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
Message-ID: <CA+zwqSoBazMgTjXAQNFvr3h0oK03t=F8hHRgtPF1XcG_GzeVPA@mail.gmail.com>

For some reason it seems that PyQt5 fails to initialize - actually the
installation probably went ok and you would just need to run the
postinstall.
If you after trying to install then execute the postinstall command in the
log file you sent and add the --silent flag it should at least install.
Do you happen to run the installer on a headless server - this is currently
unlikely to work unless you use the --silent flag.
Best,
Kristoffer

On Fri, 29 Apr 2022 at 10:22, ZHANG, bellabingbing [Student] <
bellabingbing.zhang at connect.polyu.hk> wrote:

> Dear Madam or Sir,
>
>
>
> Thanks for shareing SimNIBS , a such wonderful software to public.
>
>
>
> I am Bingbing, a Ph.D student from The Hong Kong Polytechnic University.
>
>
>
> I am trying to use SimNIBS simulate the E-fields distribution for TMS
> stimulation. When I try to install the SimNIBS to the Ubuntu Linux, it
> always failed.
>
> My path did not contain Chinese characters.
>
>
>
> Could you give me some suggestions where I am wrong?
>
>
>
> Best Regards,
>
> Bingbing
>
>
>
>
> *Disclaimer:*
>
> *This message (including any attachments) contains confidential
> information intended for a specific individual and purpose. If you are not
> the intended recipient, you should delete this message and notify the
> sender and The Hong Kong Polytechnic University (the University)
> immediately. Any disclosure, copying, or distribution of this message, or
> the taking of any action based on it, is strictly prohibited and may be
> unlawful.*
>
> *The University specifically denies any responsibility for the accuracy or
> quality of information obtained through University E-mail Facilities. Any
> views and opinions expressed are only those of the author(s) and do not
> necessarily represent those of the University and the University accepts no
> liability whatsoever for any losses or damages incurred or caused to any
> party as a result of the use of such information.*
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From bellabingbing.zhang at connect.polyu.hk  Fri Apr 29 13:12:55 2022
From: bellabingbing.zhang at connect.polyu.hk (ZHANG, bellabingbing [Student])
Date: Fri, 29 Apr 2022 11:12:55 +0000
Subject: [Simnibs-discuss] SimNIBS Installation
In-Reply-To: <CA+zwqSoBazMgTjXAQNFvr3h0oK03t=F8hHRgtPF1XcG_GzeVPA@mail.gmail.com>
References: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
 <CA+zwqSoBazMgTjXAQNFvr3h0oK03t=F8hHRgtPF1XcG_GzeVPA@mail.gmail.com>
Message-ID: <OS3P286MB1589AADDBE11BCE69F1C3E77CAFC9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>

Dear Kristoffer,
Thank you very much for your reply.

I uninstalled the Ubuntu and then reinstalled it as well as the SimNIBS.  No previous warning was shown this time, but when I run SimNIBS_gui, new error message occurred.

Is this due to that I try to run the installer on a headless server?

Best Regards,
Bingbing

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

________________________________
From: Kristoffer Madsen <kristofferm at drcmr.dk>
Sent: Friday, April 29, 2022 12:52:57 PM
To: ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk>
Cc: discuss at simnibs.org <discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] SimNIBS Installation

For some reason it seems that PyQt5 fails to initialize - actually the installation probably went ok and you would just need to run the postinstall.
If you after trying to install then execute the postinstall command in the log file you sent and add the --silent flag it should at least install.
Do you happen to run the installer on a headless server - this is currently unlikely to work unless you use the --silent flag.
Best,
Kristoffer

On Fri, 29 Apr 2022 at 10:22, ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk<mailto:bellabingbing.zhang at connect.polyu.hk>> wrote:

Dear Madam or Sir,



Thanks for shareing SimNIBS , a such wonderful software to public.



I am Bingbing, a Ph.D student from The Hong Kong Polytechnic University.



I am trying to use SimNIBS simulate the E-fields distribution for TMS stimulation. When I try to install the SimNIBS to the Ubuntu Linux, it always failed.

My path did not contain Chinese characters.



Could you give me some suggestions where I am wrong?



Best Regards,

Bingbing



[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

_______________________________________________
Simnibs-discuss mailing list
Simnibs-discuss at drcmr.dk<mailto:Simnibs-discuss at drcmr.dk>
https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.
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From kristofferm at drcmr.dk  Fri Apr 29 13:18:43 2022
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Fri, 29 Apr 2022 13:18:43 +0200
Subject: [Simnibs-discuss] SimNIBS Installation
In-Reply-To: <OS3P286MB1589AADDBE11BCE69F1C3E77CAFC9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
References: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
 <CA+zwqSoBazMgTjXAQNFvr3h0oK03t=F8hHRgtPF1XcG_GzeVPA@mail.gmail.com>
 <OS3P286MB1589AADDBE11BCE69F1C3E77CAFC9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
Message-ID: <CA+zwqSqJBuPD5R3oQhPRDc4iogzfpMq9yZM5g3YSrVeo-QPvBQ@mail.gmail.com>

Yes, the gui is unlikely to work over X-forwarding as it uses opengl
extensively, although I'd not exclude that it might work for example via
VNC etc.
However, everything should work fine on the server given that you use
script or the like to setup simulations. If you wish to use the GUI we
recommend that you install simNIBS on a personal computer to plan
simulations using the GUI.
Best,
Kristoffer

On Fri, 29 Apr 2022 at 13:13, ZHANG, bellabingbing [Student] <
bellabingbing.zhang at connect.polyu.hk> wrote:

> Dear Kristoffer,
>
> Thank you very much for your reply.
>
>
>
> I uninstalled the Ubuntu and then reinstalled it as well as the SimNIBS.
> No previous warning was shown this time, but when I run SimNIBS_gui, new
> error message occurred.
>
>
>
> Is this due to that I try to run the installer on a headless server?
>
>
>
> Best Regards,
>
> Bingbing
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
>
>
> ------------------------------
> *From:* Kristoffer Madsen <kristofferm at drcmr.dk>
> *Sent:* Friday, April 29, 2022 12:52:57 PM
> *To:* ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk
> >
> *Cc:* discuss at simnibs.org <discuss at simnibs.org>
> *Subject:* Re: [Simnibs-discuss] SimNIBS Installation
>
> For some reason it seems that PyQt5 fails to initialize - actually the
> installation probably went ok and you would just need to run the
> postinstall.
> If you after trying to install then execute the postinstall command in the
> log file you sent and add the --silent flag it should at least install.
> Do you happen to run the installer on a headless server - this is
> currently unlikely to work unless you use the --silent flag.
> Best,
> Kristoffer
>
> On Fri, 29 Apr 2022 at 10:22, ZHANG, bellabingbing [Student] <
> bellabingbing.zhang at connect.polyu.hk> wrote:
>
> Dear Madam or Sir,
>
>
>
> Thanks for shareing SimNIBS , a such wonderful software to public.
>
>
>
> I am Bingbing, a Ph.D student from The Hong Kong Polytechnic University.
>
>
>
> I am trying to use SimNIBS simulate the E-fields distribution for TMS
> stimulation. When I try to install the SimNIBS to the Ubuntu Linux, it
> always failed.
>
> My path did not contain Chinese characters.
>
>
>
> Could you give me some suggestions where I am wrong?
>
>
>
> Best Regards,
>
> Bingbing
>
>
>
>
> *Disclaimer:*
>
> *This message (including any attachments) contains confidential
> information intended for a specific individual and purpose. If you are not
> the intended recipient, you should delete this message and notify the
> sender and The Hong Kong Polytechnic University (the University)
> immediately. Any disclosure, copying, or distribution of this message, or
> the taking of any action based on it, is strictly prohibited and may be
> unlawful.*
>
> *The University specifically denies any responsibility for the accuracy or
> quality of information obtained through University E-mail Facilities. Any
> views and opinions expressed are only those of the author(s) and do not
> necessarily represent those of the University and the University accepts no
> liability whatsoever for any losses or damages incurred or caused to any
> party as a result of the use of such information.*
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
>
> *Disclaimer:*
>
> *This message (including any attachments) contains confidential
> information intended for a specific individual and purpose. If you are not
> the intended recipient, you should delete this message and notify the
> sender and The Hong Kong Polytechnic University (the University)
> immediately. Any disclosure, copying, or distribution of this message, or
> the taking of any action based on it, is strictly prohibited and may be
> unlawful.*
>
> *The University specifically denies any responsibility for the accuracy or
> quality of information obtained through University E-mail Facilities. Any
> views and opinions expressed are only those of the author(s) and do not
> necessarily represent those of the University and the University accepts no
> liability whatsoever for any losses or damages incurred or caused to any
> party as a result of the use of such information.*
>
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From bellabingbing.zhang at connect.polyu.hk  Fri Apr 29 13:34:10 2022
From: bellabingbing.zhang at connect.polyu.hk (ZHANG, bellabingbing [Student])
Date: Fri, 29 Apr 2022 11:34:10 +0000
Subject: [Simnibs-discuss] SimNIBS Installation
In-Reply-To: <CA+zwqSqJBuPD5R3oQhPRDc4iogzfpMq9yZM5g3YSrVeo-QPvBQ@mail.gmail.com>
References: <OS3P286MB1589D542685AE960A7AFAE63CAFA9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
 <CA+zwqSoBazMgTjXAQNFvr3h0oK03t=F8hHRgtPF1XcG_GzeVPA@mail.gmail.com>
 <OS3P286MB1589AADDBE11BCE69F1C3E77CAFC9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
 <CA+zwqSqJBuPD5R3oQhPRDc4iogzfpMq9yZM5g3YSrVeo-QPvBQ@mail.gmail.com>
Message-ID: <OS3P286MB158905E6B9987579B27904ACCAFC9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>

Dear Kristoffer,

Thanks so much for your prompt reply.

I have tested several command using script. It works. I also installed SimNIBS on my personal computer and I am able to using the GUI now.

Thanks again.

Best Regards,
Bingbing

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

From: Kristoffer Madsen<mailto:kristofferm at drcmr.dk>
Sent: 29 April 2022 13:18
To: ZHANG, bellabingbing [Student]<mailto:bellabingbing.zhang at connect.polyu.hk>
Cc: discuss at simnibs.org<mailto:discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] SimNIBS Installation

Yes, the gui is unlikely to work over X-forwarding as it uses opengl extensively, although I'd not exclude that it might work for example via VNC etc.
However, everything should work fine on the server given that you use script or the like to setup simulations. If you wish to use the GUI we recommend that you install simNIBS on a personal computer to plan simulations using the GUI.
Best,
Kristoffer

On Fri, 29 Apr 2022 at 13:13, ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk<mailto:bellabingbing.zhang at connect.polyu.hk>> wrote:
Dear Kristoffer,
Thank you very much for your reply.

I uninstalled the Ubuntu and then reinstalled it as well as the SimNIBS.  No previous warning was shown this time, but when I run SimNIBS_gui, new error message occurred.

Is this due to that I try to run the installer on a headless server?

Best Regards,
Bingbing

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows


From: Kristoffer Madsen <kristofferm at drcmr.dk<mailto:kristofferm at drcmr.dk>>
Sent: Friday, April 29, 2022 12:52:57 PM
To: ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk<mailto:bellabingbing.zhang at connect.polyu.hk>>
Cc: discuss at simnibs.org<mailto:discuss at simnibs.org> <discuss at simnibs.org<mailto:discuss at simnibs.org>>
Subject: Re: [Simnibs-discuss] SimNIBS Installation

For some reason it seems that PyQt5 fails to initialize - actually the installation probably went ok and you would just need to run the postinstall.
If you after trying to install then execute the postinstall command in the log file you sent and add the --silent flag it should at least install.
Do you happen to run the installer on a headless server - this is currently unlikely to work unless you use the --silent flag.
Best,
Kristoffer

On Fri, 29 Apr 2022 at 10:22, ZHANG, bellabingbing [Student] <bellabingbing.zhang at connect.polyu.hk<mailto:bellabingbing.zhang at connect.polyu.hk>> wrote:

Dear Madam or Sir,



Thanks for shareing SimNIBS , a such wonderful software to public.



I am Bingbing, a Ph.D student from The Hong Kong Polytechnic University.



I am trying to use SimNIBS simulate the E-fields distribution for TMS stimulation. When I try to install the SimNIBS to the Ubuntu Linux, it always failed.

My path did not contain Chinese characters.



Could you give me some suggestions where I am wrong?



Best Regards,

Bingbing


[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.
_______________________________________________
Simnibs-discuss mailing list
Simnibs-discuss at drcmr.dk<mailto:Simnibs-discuss at drcmr.dk>
https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

[https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg]

Disclaimer:

This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.
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